Dear Lu, Just last week I faced an almost identical problem: iMoslfm had no problem but XDS failed. I discovered, as Kay has suggested, the ORGX and ORGY values were incorrect in XDS.INP. In fact, they had essentially been swapped. If you have AUTOINDEX.INP from fast_dp, you can compare the values. For me, they were correct in AUTOINDEX.INP but incorrect in XDS.INP. I'd suggest (because it fixed the problem for me) simply swapping the values of ORGX and ORGY back, and rerunning XDS.
HTH Natalie On 12 May 2015 at 13:54, Kay Diederichs <kay.diederi...@uni-konstanz.de> wrote: > Dear LU, > > yes, your spot_15.png looks good. What worries me now is the table > > INDEX_ QUALITY DELTA XD YD X Y Z DH > DK DL > ORIGIN > > 0 0 0 1.7 0.1 997.7 1020.9 0.0010 0.0005 1.0219 > 0.38 0.51 0.25 > 0 -1 0 3.0 0.4 1002.5 1000.4 0.0026 -0.0063 1.0219 > 0.36 0.27 0.16 > 0 0 -1 3.3 0.4 972.7 1021.8 -0.0073 0.0009 1.0219 > 0.30 0.42 0.19 > 0 -1 -1 4.0 0.5 977.6 1001.3 -0.0057 -0.0059 1.0219 > 0.34 0.32 0.15 > 1 -1 0 5.2 0.4 1012.8 1027.9 0.0060 0.0029 1.0219 > 0.48 0.64 0.30 > 1 -1 -1 5.4 0.2 988.2 1028.8 -0.0022 0.0032 1.0219 > 0.58 0.75 0.38 > 0 0 1 6.0 0.5 1022.8 1019.9 0.0094 0.0002 1.0219 > 0.48 0.63 0.31 > 1 0 0 6.2 0.6 1008.1 1048.3 0.0045 0.0097 1.0219 > 0.28 0.53 0.15 > 1 0 -1 6.7 0.6 983.3 1049.2 -0.0038 0.0100 1.0219 > 0.36 0.56 0.19 > 0 -1 1 7.7 0.7 1027.5 999.4 0.0109 -0.0066 1.0219 > 0.38 0.26 0.18 > 0 1 0 7.9 0.4 992.8 1041.6 -0.0006 0.0074 1.0219 > 0.61 1.05 0.46 > 0 1 -1 9.6 0.7 967.7 1042.5 -0.0090 0.0077 1.0219 > 0.50 0.91 0.40 > 0 -1 -2 10.5 0.8 952.9 1002.3 -0.0139 -0.0056 1.0218 > 0.35 0.40 0.17 > ... > > That table is based on the assumption of ORGX=994.64 ORGY=1019.22 (the > values from the header), so IDXREF puts the origin of the reciprocal > lattice closest to these given values. However, as the table indicates, > choosing the origin at other places (columns XD YD) would result in much > lower DH DK DL, so it may well be the case that the values of ORGX ORGY are > not correct. > From the frame hg6_L1_1_00001.mccd you posted, I would rather (visually, > based on beamstop shadow) estimate ORGX ORGY to be at 980 1060 or so. > If I run (using the SPOT.XDS you posted yesterday) IDXREF with e.g. > ORGX=994.64 ORGY= 1035 then I get better indexing, and a rather clear > indication that the space group is orthorhombic: > INDEX_ QUALITY DELTA XD YD X Y Z DH > DK DL > ORIGIN > > 0 0 0 1.8 0.2 998.4 1022.2 0.0015 -0.0050 1.2019 > 0.25 0.35 0.15 > 0 -1 0 2.5 0.1 994.3 1040.4 -0.0001 0.0021 1.2019 > 0.38 0.57 0.25 > 0 0 1 3.3 0.4 977.2 1020.4 -0.0068 -0.0057 1.2019 > 0.21 0.37 0.14 > 0 -1 1 4.0 0.4 973.1 1038.5 -0.0084 0.0014 1.2019 > 0.32 0.52 0.22 > 0 0 -1 4.7 0.5 1019.7 1024.1 0.0098 -0.0043 1.2019 > 0.35 0.35 0.18 > 0 -1 -1 5.3 0.4 1015.5 1042.3 0.0082 0.0029 1.2019 > 0.45 0.62 0.28 > and > LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM & DEGREES) > CHARACTER LATTICE OF FIT a b c alpha beta gamma > > * 44 aP 0.0 64.5 93.3 116.4 90.2 90.0 90.0 > * 31 aP 0.4 64.5 93.3 116.4 89.8 90.0 90.0 > * 35 mP 1.0 93.3 64.5 116.4 90.0 90.2 90.0 > * 33 mP 4.0 64.5 93.3 116.4 90.2 90.0 90.0 > * 34 mP 4.1 64.5 116.4 93.3 90.2 90.0 90.0 > * 32 oP 4.5 64.5 93.3 116.4 90.2 90.0 90.0 > 37 mC 249.9 241.6 64.5 93.3 90.0 90.2 74.5 > > I would hypothesize that the beam position is incorrect. Personally, I'd > use > JOB= DEFPIX INTEGRATE CORRECT > ORGX=994.64 ORGY= 1035 > for a tentative round of integration, maybe together with > SPACE_GROUP_NUMBER=19 > UNIT_CELL_CONSTANTS= 64.5 93.3 116.4 90. 90.0 90.0 > and then inspect the result. If the statistics look reasonable (ISa > 10 > or so), you should optimize it (see XDSwiki). If it looks very bad (ISa < > 5), you can run > echo CENTRE | pointless XDS_ASCII.HKL > afterwards, which will tell you whether an offset in one of the indices > has to be applied. In that case, you should inspect the "INDEX ORIGIN" > table of IDXREF.LP again, to see which ORGX ORGY this corresponds to. After > this, re-integrate, optimize ... > > If you are not successful, compress your frames, upload them to some > Dropbox-like directory, and send me the link. I'll look at your data, > treating them confidentially of course, and tell you what I find. > > best, > Kay > > > > > > > >Dear Kay, > > > > I've tune these parameter for many times, and I got best results . : > > > >SPOT_RANGE=1 100 > > > >INCLUDE_RESOLUTION_RANGE=50 4.2 > > > >MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=20 > > > >but still got the same error message! > > > >The SPOT.XDS file was ploted (see attachment "spot_15.png" ), it seems > that the ice ring and beam stop shadow was excluded. But the result is > still frustrating. > > > > Best wishes! > > > >LU zuokun > -- *Natalie J. Tatum* PhD Researcher Durham University http://about.me/n.j.tatum
